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primer3-org / primer3

Primer3 is a command line tool to select primers for polymerase chain reaction (PCR).
GNU General Public License v2.0
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Add the -i option to ntthal #29

Closed nh13 closed 2 years ago

nh13 commented 4 years ago

This allows multiple queries to be performed via ntthal.

See: https://github.com/primer3-org/primer3/issues/12

nh13 commented 4 years ago

@bioinfo-ut I have tested this by piping a few hundred thousand alignments into ntthal. I could use some help with plugging in tests, as well as checking with valgrind (doesn't install on OSX 10.14).

bioinfo-ut commented 4 years ago

Our consortium's general policy requires that all new functionalities should be covered by install-time tests. Please create some tests to test the new functionality. We can't merge before that. Triinu will send you valgrind output.

nh13 commented 4 years ago

@bioinfo-ut any tips on writing tests for this functionality. This is my first PR so any suggestions would be useful.

nh13 commented 4 years ago

@bioinfo-ut tests have been added:

  1. Equivalent tests to the existing, but using the -i option.
  2. Batching many queries in one batch using the -i option.
bioinfo-ut commented 4 years ago

Valgrind error report: Unpack this .gz, run vgrep.pl (included) to see where the valgrind errors come from.

ntthal.valgrind.output.tar.gz

nh13 commented 4 years ago

@bioinfo-ut can you assign to me so I can track this?